Olamide Isreal
8887cbe592
Some checks failed
CodeQL / Analyze (python) (push) Has been cancelled
- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest - Update input/output paths to S3 (s3://omic/eureka/immunebuilder/) - Remove local mount containerOptions (not needed in k8s) - Update homepage to Gitea repo URL - Clean history to remove large model weight blobs
131 lines
3.0 KiB
Plaintext
131 lines
3.0 KiB
Plaintext
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl=2
|
|
|
|
params.fasta = 's3://omic/eureka/immunebuilder/antibody_test.fasta'
|
|
params.outdir = 's3://omic/eureka/immunebuilder/output'
|
|
params.mode = 'antibody'
|
|
params.verbose = true
|
|
params.original_weights = false
|
|
|
|
process ABODYBUILDER2 {
|
|
container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
|
|
publishDir params.outdir, mode: 'copy'
|
|
stageInMode 'copy'
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "${fasta.simpleName}.pdb", emit: structure
|
|
path "run.log", emit: logfile
|
|
|
|
script:
|
|
"""
|
|
export HOME=/home/mambauser
|
|
/opt/conda/bin/ABodyBuilder2 \\
|
|
-f ${fasta} \\
|
|
-o ${fasta.simpleName}.pdb \\
|
|
${params.verbose ? '-v' : ''} 2>&1 | tee run.log
|
|
"""
|
|
}
|
|
|
|
process NANOBODYBUILDER2 {
|
|
container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
|
|
publishDir params.outdir, mode: 'copy'
|
|
stageInMode 'copy'
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "${fasta.simpleName}.pdb", emit: structure
|
|
path "run.log", emit: logfile
|
|
|
|
script:
|
|
"""
|
|
export HOME=/home/mambauser
|
|
/opt/conda/bin/NanoBodyBuilder2 \\
|
|
-f ${fasta} \\
|
|
-o ${fasta.simpleName}.pdb \\
|
|
${params.verbose ? '-v' : ''} 2>&1 | tee run.log
|
|
"""
|
|
}
|
|
|
|
process TCRBUILDER2 {
|
|
container 'harbor.cluster.omic.ai/omic/immunebuilder:latest'
|
|
publishDir params.outdir, mode: 'copy'
|
|
stageInMode 'copy'
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "${fasta.simpleName}.pdb", emit: structure
|
|
path "run.log", emit: logfile
|
|
|
|
script:
|
|
"""
|
|
export HOME=/home/mambauser
|
|
/opt/conda/bin/TCRBuilder2 \\
|
|
-f ${fasta} \\
|
|
-o ${fasta.simpleName}.pdb \\
|
|
${params.verbose ? '-v' : ''} \\
|
|
${params.original_weights ? '--original_weights' : ''} 2>&1 | tee run.log
|
|
"""
|
|
}
|
|
|
|
workflow PREDICT_ANTIBODY {
|
|
take:
|
|
fasta_ch
|
|
|
|
main:
|
|
ABODYBUILDER2(fasta_ch)
|
|
|
|
emit:
|
|
structure = ABODYBUILDER2.out.structure
|
|
logfile = ABODYBUILDER2.out.logfile
|
|
}
|
|
|
|
workflow PREDICT_NANOBODY {
|
|
take:
|
|
fasta_ch
|
|
|
|
main:
|
|
NANOBODYBUILDER2(fasta_ch)
|
|
|
|
emit:
|
|
structure = NANOBODYBUILDER2.out.structure
|
|
logfile = NANOBODYBUILDER2.out.logfile
|
|
}
|
|
|
|
workflow PREDICT_TCR {
|
|
take:
|
|
fasta_ch
|
|
|
|
main:
|
|
TCRBUILDER2(fasta_ch)
|
|
|
|
emit:
|
|
structure = TCRBUILDER2.out.structure
|
|
logfile = TCRBUILDER2.out.logfile
|
|
}
|
|
|
|
workflow {
|
|
if (!params.fasta) {
|
|
error "Please provide input FASTA file(s) using --fasta parameter"
|
|
}
|
|
|
|
fasta_ch = Channel.fromPath(params.fasta, checkIfExists: true)
|
|
|
|
if (params.mode == 'antibody') {
|
|
PREDICT_ANTIBODY(fasta_ch)
|
|
} else if (params.mode == 'nanobody') {
|
|
PREDICT_NANOBODY(fasta_ch)
|
|
} else if (params.mode == 'tcr') {
|
|
PREDICT_TCR(fasta_ch)
|
|
} else {
|
|
error "Invalid mode: ${params.mode}. Please use 'antibody', 'nanobody', or 'tcr'"
|
|
}
|
|
}
|